Backgrounds: There is growing evidence from both observational and intervention studies that Whole Grain (WG) cereals exert beneficial effects on human health, especially on the metabolic profile. The aim of this study was to perform a meta-analysis of randomised controlled trials (RCT) to assess the acute and medium/long-term effect of WG foods on glycaemic control and insulin sensitivity in healthy individuals. Methods: A search for all the published RCT on the effect of WG food intake on glycaemic and insulin response was performed up to December 2016. Effect size consisted of mean difference (MD) and 95% CI between the outcomes of intervention and the control groups using the generic inverse-variance random effects model. Results: The meta-analysis of the 14 studies testing the acute effects of WG foods showed significant reductions of the post-prandial values of the glucose iAUC (0–120 min) by −29.71 mmol min/L (95% CI: −43.57, −15.85 mmol min/L), the insulin iAUC (0–120 min) by −2.01 nmol min/L (95% CI: −2.88, −1.14 nmol min/L), and the maximal glucose and insulin response. In 16 medium- and long-term RCTs, effects of WG foods on fasting glucose and insulin and homeostatic model assessment-insulin resistance values were not significant. Conclusions: The consumption of WG foods is able to improve acutely the postprandial glucose and insulin homeostasis compared to similar refined foods in healthy subjects. Further research is needed to better understand the long-term effects and the biological mechanisms.